Thank u for reply. I did energy minimization and equilibration step. It converged in 696 steps which is shown below.
Step= 692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03, atom= 2099 Step= 693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax= 9.72038e+03, atom= 2099 Step= 695, Dmax= 6.6e-03 nm, Epot= -7.12670e+05 Fmax= 9.39830e+02, atom= 2099 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 696 steps Potential Energy = -7.1266969e+05 Maximum force = 9.3982965e+02 on atom 2099 Norm of force = 2.1967674e+01 # md.mdp file title = protein cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1000000 ; total 50 ps. nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 0.1 0.1 tc-grps = protein ZN IMP sol NA+ ref_t = 300 300 300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 # pr.mdp file title = protein cpp = /lib/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 50000 ; total 20.0 ps. nstcomm = 1 nstxout = 250 ; output coordinates every 0.5 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = V-rescale tau_t = 0.1 0.1 0.1 0.1 0.1 tc_grps = protein ZN sol IMP NA+ ref_t = 300 300 300 300 300 ; Pressure coupling is on Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 #em.mdp file title = protein cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 I need further help to trouble shoot this problem. On Sat, Dec 3, 2011 at 10:46 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > pragna lakshmi wrote: > >> Hi, >> I am trying to run protein-ligand complex simulation. At the final MD >> run step it is showing the following error. Can anybody tell me the >> solution for this error? >> >> > http://www.gromacs.org/**Documentation/Errors#LINCS.** > 2fSETTLE.2fSHAKE_warnings<http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings> > > There are hundreds of threads in the archive with the same issue and > several possible solutions. Please consult the link above (and referenced > pages), as well as other posts. > > If you need further help diagnosing the problem, please post a complete > .mdp file, as well as a description of prior minimization and equilibration. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- T.Pragna Lakshmi, Junior Scientist, Vision Research Center, Sankara Netralaya, Chennai, India. Pin: 600006.
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